Contamination of the amorphous carbon layer during milling by residue of a metal mask may occur when using a metal sub-layer to transfer a pattern image from an imprinted resist to the magnetic layer. The residue of metal contaminates the amorphous carbon mask layer, resulting in affection of control dimensions bias and fidelity of patterning. Size and position control of features during a pattern fabrication process degrades drastically due to metallic residue mixed up with amorphous carbon mask layer residue left after stack patterning. Also, such a mixture is hard to clean up without affecting magnetic properties of the magnetic layer.